Studies in the Human Immunogenetics Research Section concern the T cell receptor (TCR) repertoire in healthy individuals and how it is modulated by exposure to infectious agents or by disease. The extensive diversity of the mammalian T cell receptor (TCR) repertoire is generated by the somatic rearrangement of non-contiguous germline variable, diversity and junctional gene segments. Detailed knowledge of the extent and diversity of the TCR repertoire used in specific immune responses will facilitate our ability to understand the role of TCR genes in immune responses in normal and disease states. TCR spectratype provides a global survey of the expressed TCR repertoire by displaying the distributions of complementarity determining region-3 (CDR3) lengths for each of the TCR alpha (A) and beta (B) variable (V) gene families. Because the CDR3 region of the TCR is a primary determinant of the fine antigenic specificity of the T lymphocyte, analysis of this region can yield considerable insight into the molecular basis of a T cell response. Studies of humans, macaques, and mice reveal that TCRA and TCRB spectratype profiles from all species have common features. Distributions of CDR3 lengths for both TCRA and TCRB transcripts show a Gaussian distribution with a mean CDR3 length corresponding to 10-12 amino acids. A statistical test was applied to the data to determine the extent to which a given spectratype profile deviated from an idealized Gaussian distribution (Hamming distance-HD). CD4+ T cells showed profiles that most closely resembled Gaussian distributions thus mean HD values for profiles of CD4+ T cells were used to establish criteria for identification of skewed profiles. Overall CD8+ T cells were more skewed than CD4+ T cells and double negative (DN: CD4-CD8- CD3+) T cells in humans and double-positive (DP: CD4+ and CD8+) T cells in macaques were the most skewed T cell populations. Testing multiple samples over time from humans and macaques showed similar profiles for a given TCRV family over time. The presence of an over represented CDR3 length within a profile was observed on multiple testing. In order to determine whether a peak corresponded to a clonal expansion, sequence analyses was performed. In most cases, a predominant sequence was observed to correspond to a peak in a spectratype profile. In humans, unusual populations of DN T cells that express invariant or conserved TCRAV4A, AV7, AV19, and AV24 chains were identified. Each of the conserved TCRA families was over-represented in greater than 70% of the individuals studied and all individuals expressed at least one of the over-represented TCRAV families with stability over time. Autoimmune Lymphoproliferative Syndrome (ALPS) is an inherited disease with defects in lymphocyte apoptosis. Expanded clonal populations of TCRA were observed in both the CD4+ and DN subsets and clonal expansions were also observed in CD8+ and DN subsets. ALPS patients have a defect in apoptosis and therefore accumulate DN T cells. In contrast, none of the invariant or conserved TCRA were observed DN cells from ALPS patients. These studies reveal different pathways for the development of the conserved or invariant TCRA and conventional T lymphocytes. Our knowledge of the TCRB repertoire of macaques was extended by the cloning of full length transcripts and sequence analyses of 8 new TCRBV families. The full repertoire of macaque TCRBV families has now been sequenced. The long term studies of the dynamics of the TCRB repertoire in rhesus macaques infected with SIV continue. Observations to date include detection of clonal populations of T lymphocytes expanded in CD4+ or CD8+ T cell subpopulations. An animal model for the human severe combined immunodeficiency disease (SCID) caused by Adenosine Deaminase (ADA) deficiency has been developed. Human patients and the knock out mice are severely immunodeficient and have markedly decreased numbers of peripheral lymphocytes. The lymphocytes that are present have not been characterized for either the extent or the nature of diversity in the TCR. The TCR repertoire of parental strains was determined and C57Bl/6 and 129 strains have different numbers of functional TCRBV gene segments. These differences make it possible type offspring for TCRB haplotype in order to analyze their expressed TCRB repertoire.